Tag: PPI

RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder

Significance Hairpin pyrrole-imidazole (Py-Im) polyamides can be programmed to bind a broad repertoire of DNA sequences. Py-Im small molecules can be used to target cancer-specific coding regions and block transcription elongation. This transcription blockage by Py-Im cannot be rescued by transcription elongation factors, such as TFIIS. The mechanism by which…

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Predicting sepsis severity at first clinical presentation: The role of endotypes and mechanistic signatures

Summary Background Inter-individual variability during sepsis limits appropriate triage of patients. Identifying, at first clinical presentation, gene expression signatures that predict subsequent severity will allow clinicians to identify the most at-risk groups of patients and enable appropriate antibiotic use. Methods Blood RNA-Seq and clinical data were collected from 348 patients…

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Immune-related Prognostic Genes of ccRCC

Introduction Kidney cancer is one of the most commonly diagnosed tumors around the globe.1 According to the statistics from the World Health Organization, annually, there are more than 140,000 RCC-related deaths.2 ccRCC is the most typical subtype of kidney cancer and contributes to the majority of kidney cancer-related deaths.3,4 Until…

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Bioinformation Analysis Reveals IFIT1 as Potential Biomarkers in Centr

Introduction Tuberculosis (TB) is considered to be one of the top ten causes of death in the world, about a quarter of the world’s population is infected with M. tuberculosis.1 The World Health Organization (WHO) divides tuberculosis into pulmonary tuberculosis (PTB) and extra-pulmonary tuberculosis (EPTB). Although breakthroughs have been made…

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Crosstalk between Venous Thromboembolism and Periodontal Diseases: A Bioinformatics Analysis

This article was originally published here Dis Markers. 2021 Dec 10;2021:1776567. doi: 10.1155/2021/1776567. eCollection 2021. ABSTRACT BACKGROUND: This current study applied bioinformatics analysis to reveal the crosstalk between venous thromboembolism (VTE) and periodontitis, as well as the potential role of immune-related genes in this context. METHODS: Expression data were downloaded…

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Adrenal aldosterone-producing adenoma | IJGM

Background Primary hyperaldosteronism (PA) is characterized by spontaneous secretion of excessive aldosterone and inhibition of plasma renin activity.1 The pathogenesis of adrenal aldosterone-producing adenoma (APA) involves the abnormal proliferation of adrenal cortex cells and the excessive secretion of aldosterone, accounting for nearly 30% of PA. Excessive secretion of aldosterone can…

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Establishment of sunitinib-resistant CDX model of ccRCC

Introduction Renal cell carcinoma (RCC) accounts for approximately 2–3% of all malignant tumors, and its prevalence is rising. Metastatic RCC accounts for 25–30% of all RCC cases, and has an exceedingly poor prognosis.1 In 2020, among approximately 430,000 newly discovered cases of RCC, 179,000 died.2 Clear cell renal cell carcinoma…

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Prognosis Biomarkers via WGCNA in HCC

Introduction According to the cancer statistics reported in 2020, hepatocellular carcinoma (HCC) is the main type of Primary Carcinoma of the Liver and the second leading causes of cancer-related death globally, with a five-year survival rate < 20%.1 Currently, surgical resection, a standard therapy for HCC, contributes to the prognosis…

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Identification of Hub Genes in Patients with Alzheimer Disease and Obs

Introduction Alzheimer’s disease (AD) ranks first among the common dementia type of the world. According to epidemiological investigation from the International Alzheimer’s disease association, about 45 million people has been suffered from AD, and the number is expected to increase to 131 million in 2050.1 Despite the widespread prevalence of…

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Identification of lipid metabolism-associated gene signature

Background Female breast cancer has surpassed lung cancer as the most commonly diagnosed cancer. Despite the dramatic improvement in breast cancer prognosis due to recent therapeutic advances, such as more effective adjuvant and neo-adjuvant chemotherapies, together with more radical and safer surgery, advances in early diagnosis and treatment over the…

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Detecting Spatially Co-expressed Gene Clusters with Functional Coherence by Graph-regularized Convolutional Neural Network

This article was originally published here Bioinformatics. 2021 Dec 2:btab812. doi: 10.1093/bioinformatics/btab812. Online ahead of print. ABSTRACT MOTIVATION: Clustering spatial-resolved gene expressions is an essential analysis to reveal gene activities in the underlying morphological context by their functional roles. However, conventional clustering analysis does not consider gene expression co-localizations in…

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Identification of circRNA-miRNA-mRNA Regulatory Network and Autophagy Interaction Network in Atrial Fibrillation Based on Bioinformatics Analysis

Background: Circular RNA (circRNA) has been receiving increased attention in the research of atrial fibrillation (AF). Our study aims to find potential circRNAs and identify the circRNA-miRNA-mRNA regulatory network in AF based on bioinformatics analysis. Methods: GSE129409 was retrieved from the Gene Expression Omnibus (GEO) database, and we used R…

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Potenial biomarker in Crohn’s diease via bioinformatics

Introduction Crohn’s disease (CD) and ulcerative colitis are chronic inflammatory disorders of the gastrointestinal tract, with symptoms evolving in a relapsing and remitting manner that comprise the term inflammatory bowel disease (IBD).1 CD is characterized by the involvement of all parts of the intestine, the most common being the terminal…

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The Construction and Comprehensive Analysis of a ceRNA Immunoregulator

1Department of Cardiology, Xiangtan Central Hospital, Xiangtan, Hunan, People’s Republic of China; 2Department of Cardiology, Guangxi Cardiovascular Institute, The First Affiliated Hospital of Guangxi Medical University, Guangxi, People’s Republic of China; 3Department of Critical Care Medicine, Zhuzhou Central Hospital, Zhuzhou, Hunan, People’s Republic of China Correspondence: Yiqian ZengDepartment of Critical…

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Comprehensive analysis of ceRNA networks to determine genes related to prognosis, overall survival, and immune infiltration in clear cell renal carcinoma

Comput Biol Med. 2021 Nov 20:105043. doi: 10.1016/j.compbiomed.2021.105043. Online ahead of print. ABSTRACT BACKGROUND: Clear cell renal cell carcinoma (ccRCC) is one of the common subtypes of kidney cancer. Circular RNAs (circRNAs) act as competing endogenous RNAs (ceRNAs) to affect the expression of microRNAs (miRNAs), and hence the expression of…

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Construction of a circRNA-miRNA-mRNA Regulated Pathway Involved in EGFR-TKI Lung Adenocarcinoma Resistance

1 Introduction Lung cancer is the leading cause of cancer-related deaths worldwide, with adenocarcinoma as the most common histological subtype.1 In recent years, epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs), such as gefitinib (first generation) and osimertinib (third generation), have been widely used for lung adenocarcinoma patients harboring activated EGFR…

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Bioinformatics analysis pinpoints the pathways involved in intestinal SARS/CoV-2 infection

Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) is a positive-strand RNA virus, which appears spherical under a transmission electron microscope. Many studies have shown that SARS-CoV-2 infects host cells via the interaction between the viral spike protein and the host receptor, angiotensin-converting enzyme II (ACE2). SARS-CoV-2 can spread through…

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WGCNA Analysis Identifies Polycystic Ovary Syndrome-Associated Circula

Introduction Polycystic ovary syndrome (PCOS) is a common endocrine metabolic disorder in women of childbearing age.1 PCOS patients are typically characterized by androgen excess, polycystic ovaries and anovulation, and are often accompanied by insulin resistance and obesity.2 Consequently, patients with this syndrome not only suffer from infertility,3 but also have…

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Bioinformatics Full Time Govt. jobs in Bethesda

Broaden your search Bioinformatics, Full Time, Govt., Bethesda, Maryland 1 Life Sciences, Full Time, Govt., Senior Scientist, Bethesda, Maryland 1 Bioinformatics, Full Time, Govt., Senior Scientist, Maryland 1 Refine your search To see more jobs like this, please sign up…

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Science: AlphaFold teamed up with RoseTTAFold to surpass another big mountain in protein structure prediction

The artificial intelligence (AI) revolution in the field of protein structure prediction continues. At the end of 2020, the new generation of AlphaFold (AlphaFold2) developed by DeepMind has solved the major challenges in the biological field for decades and achieved a major breakthrough in accurately predicting the 3D structure of…

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circRNA-miRNA-mRNA regulatory network in atrial fibrillation

Introduction Atrial fibrillation (AF) is the most common type of arrhythmia in clinical practice, with global prevalence continuing to increase primarily with age.1 In China, 6.5 persons out of every thousand suffer from AF, and there are about 3.9 million patients with AF who are over 60 years old, but…

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KEGG ENZYME: 2.6.1.57

Entry EC 2.6.1.57                 Enzyme                                  Name aromatic-amino-acid transaminase;aromatic amino acid aminotransferase;aromatic aminotransferase;ArAT Class Transferases;Transferring nitrogenous groups;TransaminasesBRITE hierarchy Sysname aromatic-amino-acid:2-oxoglutarate aminotransferase Reaction(IUBMB) an aromatic amino acid + 2-oxoglutarate = an aromatic oxo acid + L-glutamate [RN:R03120] Reaction(KEGG) R03120 > R00694 R00734 R10845; (other) R01731 R07396 Reaction Substrate aromatic amino acid [CPD:C01021]; 2-oxoglutarate [CPD:C00026] Product…

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Genes and Pathways Involved in Postmenopausal Osteoporosis

Introduction Many postmenopausal women suffer from postmenopausal osteoporosis (PMO). A survey of 3247 Italian postmenopausal women found that according to bone mineral density (BMD) diagnostic criteria, the prevalence of osteoporosis was 36.6%.1 PMO patients may suffer from chronic pain and fractures, and as a result their quality of life is…

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Bioinformatics Pharma jobs in Pearl River

Broaden your search Bioinformatics, Pearl River, New York 1 Life Sciences, Pharma, Pearl River, New York 15 Bioinformatics, All Industry, Pearl River, New York 1 Bioinformatics, Pharma, New York 1 Refine your search To see more jobs like…

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ARGs as potential biomarkers & therapeutic targets in AF

Introduction Atrial fibrillation (AF) is the most common clinically sustained cardiac rhythm disorder. There is a high prevalence of AF all over the world, the highest in North America, Europe, China, and Southeast Asia, with approximately 270–360 cases per 100,000 people.1 Due to the lack of understanding of the pathogenesis…

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Candidate genes associated with synovial macrophages

Jia Xu,1 Ming-Ying Zhang,2 Wei Jiao,1 Cong-Qi Hu,1 Dan-Bin Wu,2 Jia-Hui Yu,1 Guang-Xing Chen2,3 1First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, 510405, Guangdong, People’s Republic of China; 2Department of Rheumatology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510405, Guangdong, People’s Republic of China;…

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Bioinformatics analysis to screen DNA methylation-driven genes for prognosis of patients with bladder cancer

This article was originally published here Transl Androl Urol. 2021 Sep;10(9):3604-3619. doi: 10.21037/tau-21-326. ABSTRACT BACKGROUND: Bladder cancer (BLCA) is the most prevalent tumor affecting the urinary system, and has contributed to a rise in morbidity and mortality rates. Herein, we sought to identify the methylation-driven genes (MDGs)of BLCA in an…

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Identification of Significant Genes in Lung Cancer of Nonsmoking Women via Bioinformatics Analysis

This article was originally published here Biomed Res Int. 2021 Oct 11;2021:5516218. doi: 10.1155/2021/5516218. eCollection 2021. ABSTRACT BACKGROUND: The aim of this study was to identify potential key genes, proteins, and associated interaction networks for the development of lung cancer in nonsmoking women through a bioinformatics approach. METHODS: We used…

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Identification of Hub mRNAs and lncRNAs in Atrial Fibrillation Using Weighted Co-expression Network Analysis With RNA-Seq Data

This article was originally published here Front Cell Dev Biol. 2021 Oct 4;9:722671. doi: 10.3389/fcell.2021.722671. eCollection 2021. ABSTRACT Atrial fibrillation (AF)/paroxysmal AF (PAF) is the main cause of cardiogenic embolism. In recent years, the progression from paroxysmal AF to persistent AF has attracted more and more attention. However, the molecular…

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A TME-Related Signature as a Biomarker in Liver Cancer

Introduction As one of the most frequent causes of cancer deaths across the globe, liver cancer, characterized by high mortality, recurrence, metastasis and poor prognosis, is the only one of the top five deadliest cancers to have an annual percentage increase in occurrence.1 Surgery, local destructive therapies, and liver transplantation…

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Identification of antineoplastic agents for oral squamous cell carcinoma: an integrated bioinformatics approach using differential gene expression and network biology

Abstract Oral squamous cell carcinoma (OSCC) is the most common malignant epithelial neoplasm and anatomical subtype of head and neck squamous cell carcinoma (HNSCC) with an average 5-year survival rate of less than 50%. To improve the survival rate of OSCC, the discovery of novel anti-cancer drugs is urgently needed….

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Identification of immunization-related new prognostic biomarkers for papillary renal cell carcinoma by integrated bioinformatics analysis

This article was originally published here BMC Med Genomics. 2021 Oct 7;14(1):241. doi: 10.1186/s12920-021-01092-w. ABSTRACT BACKGROUND: Despite papillary renal cell carcinoma (pRCC) being the second most common type of kidney cancer, the underlying molecular mechanism remains unclear. Targeted therapies in the past have not been successful because of the lack…

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Quantitative PCR assay for detection of Helicobacter pylori

Introduction Helicobacter pylori is a common pathogen that infects nearly 50% of the global population.1 Infection with this pathogen causes chronic gastritis, which can cause chronic gastroduodenal diseases such as gastritis, gastric ulcer, duodenal ulcer, gastric cancer, and gastric mucosa-associated lymphoid tissue (MALT) B-cell lymphoma.2 Although H. pylori is the…

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KEGG ENZYME: 2.7.1.90

Entry EC 2.7.1.90                 Enzyme                                  Name diphosphate—fructose-6-phosphate 1-phosphotransferase;6-phosphofructokinase (pyrophosphate);pyrophosphate-fructose 6-phosphate 1-phosphotransferase;inorganic pyrophosphate-dependent phosphofructokinase;inorganic pyrophosphate-phosphofructokinase;pyrophosphate-dependent phosphofructo-1-kinase;pyrophosphate-fructose 6-phosphate phosphotransferase Class Transferases;Transferring phosphorus-containing groups;Phosphotransferases with an alcohol group as acceptorBRITE hierarchy Sysname diphosphate:D-fructose-6-phosphate 1-phosphotransferase Reaction(IUBMB) diphosphate + D-fructose 6-phosphate = phosphate + D-fructose 1,6-bisphosphate [RN:R00764] Reaction(KEGG) Substrate diphosphate [CPD:C00013]; D-fructose 6-phosphate [CPD:C00085] Product phosphate [CPD:C00009]; D-fructose…

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How to calculate the risk ratio(Enrichment) of mutations on interaction interfaces

How to calculate the risk ratio(Enrichment) of mutations on interaction interfaces 0 Hi there, I’m doing a study about the impact of mutations on the interaction interface of proteins, and I need to calculate the risk ratio between the disease group and the control group. I found a published paper…

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structure aware protein interaction site prediction based on depth map convolution network

This paper is published in… By Zhou Yaoqi research group of Shenzhen Graduate School of Peking University and Yang Yuedong research group of Sun Yat sen University Bioinformatics Articles on . Address of thesis :https://doi.org/10.1093/bioinformatics/btab643 Abstract protein – Protein interactions (PPI) It plays a vital role in many biological processes…

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Quercetin inhibits the proliferation of multiple myeloma cells by upregulating PTPRR expression

This article was originally published here Acta Biochim Biophys Sin (Shanghai). 2021 Sep 24:gmab128. doi: 10.1093/abbs/gmab128. Online ahead of print. ABSTRACT Multiple myeloma (MM) is an incurable disease characterized by malignant plasma cell clonal expansion in the bone marrow; therefore, inhibiting the proliferation of plasma cells is an important approach…

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miRNAs and mRNAs in intestinal ischemia-reperfusion injury

Introduction Intestinal ischemia-reperfusion (II/R) injury is a severe clinical complication common in the Intensive Care Unit (ICU). It is associated with high morbidity and mortality.1 Usually, this problem is followed by various causes, including sepsis, shock, trauma, and so on.2 Intestinal ischemia-reperfusion injury destroys intestinal tissue and impairs the function…

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PPI-Network igraph for tissue-specific data

PPI-Network igraph for tissue-specific data 0 I am new to bioinformatics in general and would really appreciate some help with the project Im working on. My data of protein-protein interactions is constructed in a table (stored in MySQL) with binary information about tissue-specificity. Now I am trying to create an…

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BLASTP version 4 database error *Help

I am having trouble running the blastp command. When I run this command against the Swiss-prot database installed from the NCBI i get this error $ blastp -db swissprot -query Ecoli_rpoB.fasta -out TEST15.txt BLAST Database error: Error: Not a valid version 4 database. However, when I create my own database…

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Identification of Prognosis-Associated Biomarkers in Thyroid Carcinoma

Introduction Thyroid cancer (TC) is a common endocrine malignancy with a rapidly increasing incidence worldwide, and the estimated new cases and deaths are notably higher in women than in men.1 Papillary thyroid carcinoma (PTC) is identified as the most common pathological type of TC, and accounts for approximately 80–85% of…

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Bioconductor – PPInfer

DOI: 10.18129/B9.bioc.PPInfer     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see PPInfer. Inferring functionally related proteins using protein interaction networks Bioconductor version: 3.12 Interactions between proteins occur in many, if not most, biological processes. Most proteins perform their functions in networks associated…

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Gene Expression Analysis Reveals Key Genes and Signalings Associated with the Prognosis of Prostate Cancer

This article was originally published here Comput Math Methods Med. 2021 Aug 28;2021:9946015. doi: 10.1155/2021/9946015. eCollection 2021. ABSTRACT It is urgent to identify novel biomarkers for prostate cancer (PCa) prognosis and to understand the mechanisms regulating the tumorigenesis for PCa treatment. In this study, GSE17951 and TCGA were used to…

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Network analysis using distinct centrality measurements

Network analysis using distinct centrality measurements 0 Hello to everyone, I have question regarding to network analysis. Currently, I’m conducting this kind of analysis using data retrieved from STRING db to obtain highly central nodes. I have re-constructed the network in R using the igraph package to subsequently proceed with…

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GitHub – HaoWuLab-Bioinformatics/wu-group: ECSWalk

GitHub – HaoWuLab-Bioinformatics/wu-group: ECSWalk Files Permalink Failed to load latest commit information. Type Name Latest commit message Commit time ECSWalk: A carcinogenic driver module detection method based on a network model. Data used in this study: In our research, we used data processed by Rafsan Ahmed, et al. and Mark…

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Gene expression profiling of contralateral dorsal root gangl

Introduction Mirror-image pain (MIP) is a mysterious pain phenomenon which is accompanied with many clinical pain conditions.1 MIP develops from the healthy body region which is contralateral to the actual injured site.1–3 MIP is typically characterized by increased mechanical hypersensitivity on the uninjured mirror-image body side.4 It can be triggered…

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PROPER-Seq Uses NGS to ID Undiscovered Protein-Protein Interactions

NEW YORK – A new method for profiling protein-protein interactions (PPIs) using next-generation sequencing as a readout has the potential to reveal thousands of previously undiscovered combinations in human cells. The method, called PROPER-seq (protein-protein interaction sequencing), tags proteins with RNA barcodes that form chimeric sequences when brought into proximity with…

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Problem of visualizing results of PPI network

Problem of visualizing results of PPI network 0 Hi,I want to visualize my PPI network into cytoscape or Network analyst .But my ppI node are 661 and edges are 680 and seeds are 15.So i feel problem of visualizing it into cytoscape or Network analyst.Because of huge number of nodes…

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Multiform antimicrobial resistance from a metabolic mutation

Abstract A critical challenge for microbiology and medicine is how to cure infections by bacteria that survive antibiotic treatment by persistence or tolerance. Seeking mechanisms behind such high survival, we developed a forward-genetic method for efficient isolation of high-survival mutants in any culturable bacterial species. We found that perturbation of…

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Helicobacter pylori in Pakistan | IDR

Introduction Helicobacter pylori, an infectious agent of human chronic active gastritis and also associated with other gastric ailments such as peptic ulcer, gastric cancer, and mucosa-associated lymphoid tissue lymphoma.1 Clarithromycin is considered the best option among other antibiotics for the management of this bacterial infection.2 However, increasing resistance against this…

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How can I get the exact 3D structure of the protein to use the PDB file for PPI docking

How can I get the exact 3D structure of the protein to use the PDB file for PPI docking 1 I am working on an uncharacterized protein, and I need to know its PPI with rna polymrase in humans. Please, how can I get the exact 3D structure of the…

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